Methods of using mass spectrometry for the measurement of established and candidate biomarker proteins could benefit from improvements in methods for the preparation, handling and quantitative performance of stable isotope labeled peptides. Such labeled peptides are used as internal standards in the analysis of peptides samples, including protein sample digests, by mass spectrometry. In a specific case, the art could benefit from improvements to the performance of the technology called “SISCAPA” that was disclosed in one or more of the patent filings referenced above, and a number of recent publications including, for instance: An effective and rapid method for functional characterization of immunoadsorbents using POROS® beads and flow cytometry, N. Leigh Anderson et al., Journal of Proteome Research 3:228-34 (2004); Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA), Anderson, N. L. et al., Journal of Proteome Research 3: 235-44 (2004); Anti-peptide antibody screening: selection of high affinity monoclonal reagents by a refined surface plasmon resonance technique, Matthew E. Pope et al., J. Immunol. Methods, 341(1-2):86-96 (2009); A Human Proteome Detection and Quantitation Project: hPDQ, N. Leigh Anderson, et al., Mol. Cell. Proteomics 8:883-886 (2009); SISCAPA Peptide Enrichment on Magnetic Beads Using an Inline Beadtrap Device, N. Leigh Anderson, et al., Mol. Cell. Proteomics 8:995-1005 (2009); An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers, Jeffrey R. Whiteaker, et al., Mol. Cell. Proteomics 9:184-196 (2010); Proteomic-Based Multiplex Assay Mock Submissions: Supplementary Material to A Workshop Report by the NCI-FDA Interagency Oncology Task Force on Molecular Diagnostics, Fred E. Regnier, et al., Clin. Chem. 56:2 165-171 (2010); MALDI Immunoscreening (MiSCREEN): A Method for Selection of Anti-peptide Monoclonal Antibodies for Use in Immunoproteomics, Morteza Razavi, Matthew E. Pope, Martin V. Soste, Brett A. Eyford, N. Leigh Anderson and Terry W. Pearson, Journal of Immunological Methods 364:50-64 (2011).